Methods and Compositions for Tagging and Identifying Polynucleotides

ABSTRACT

The invention provides methods and compositions for attaching oligonucleotide tags to polynucleotides for the purpose of carrying out analytical assays in parallel and for decoding the oligonucleotide tags of polynucleotides selected in such assays. Words, or subunits, of oligonucleotide tags index submixtures in successively more complex sets of submixtures (referred to herein as “tiers” of submixtures) that a polynucleotide goes through while successive words are added to a growing tag. By identifying each word of an oligonucleotide tag, a series of submixtures is identified including the first submixture that contains only a single polynucleotide, thereby providing the identity of the selected polynucleotide. The analysis of the words of an oligonucleotide tag can be carried out in parallel, e.g. by specific hybridization of the oligonucleotide tag to its tag complement on an addressable array; or such analysis can be carried out serially by successive specific hybridizations of labeled word complements, or the like.

This application is a continuation-in-part of U.S. patent applicationSer. No. 11/055,187 filed 10 Feb. 2005, which is incorporated byreference in its entirety; this application also claim priority formU.S. provisional patent application Ser. No. 60/662,167 filed 16 Mar.2005, which is incorporated by reference in its entirety.

FIELD OF THE INVENTION

The present invention relates to methods and compositions for analyzingpopulations of polynucleotides, and more particularly, to methods andcompositions for attaching oligonucleotide tags to polynucleotides andfor identifying such polynucleotides by detection of the attached tag.

BACKGROUND

Oligonucleotide tags have frequently been employed to label and sortpolynucleotides in analytical molecular biology, e.g. Brenner et al,Proc. Natl. Acad. Sci., 97: 1665-1670 (2000); Church et al, Science,240: 185-188 (1988); Shoemaker et al, Nature Genetics, 14: 450-456(1996); Hardenbol et al, Nature Biotechnology, 21: 673-678 (2003); andthe like. The benefits of conducting analytical reactions with suchmolecular tags include (i) achievement of high degrees of multiplexingso that many analytes can be measured in the same reaction mixture withconservation of rare or expensive reagents, and (ii) ability to designoligonucleotide tags to optimize assay sensitivity, convenience, cost,and multiplexing capability. In most approaches, oligonucleotide tagsare attached to polynucleotide analytes or probes in separate reactions,after which they are combined for multiplexed reactions, e.g. Church etal (cited above); Shoemaker et al (cited above); Hardenbol et al (citedabove); Wallace, U.S. Pat. No. 5,981,176; and the like. Alternatively,unique oligonucleotide tags have also been attached to sets ofpolynucleotides in the same reaction by first forming a population ofconjugates with a much larger set of oligonucleotide tags followed byremoving a sample of polynucleotides (small in size relative to theoligonucleotide tag population), e.g. Brenner et al (cited above); Maoet al, International patent publication WO 02/097113. In the formerapproach, each analyte or probe may be identified in parallel by readingits oligonucleotide tag (whose sequence is known) in a single operation,e.g. by hybridization to a microarray. While such a readout is extremelyefficient, the initial cost of synthesizing and separately labeling theanalytes or probes is high. In the latter approach, the cost ofattaching tags is low; however, the identity of the oligonucleotide tagattached to a given analyte or probe (even though unique) is unknown, soits use is limited to shuttling information about its probe or analyteto a readout platform.

It would be highly useful if a tagging method were available in whichprobes or analytes could each be uniquely labeled with anoligonucleotide tag in one or a few multiplex reactions employing a fewtagging reagents, such that the resulting tags could be readilyidentified by a simple decoding procedure. Such a method would have thebenefits both of the approach of separately attaching oligonucleotidetags (facile identification) and the approach of attachingoligonucleotide tags in multiplex reactions (less expense). Such atagging method would find applications in many fields of scientific andbiomedical research, particularly in genetics and cancer research whereit is frequently necessary or desirable to analyze large numbers ofpolynucleotide analytes in rare or expensive samples.

SUMMARY OF THE INVENTION

The present invention provides a method and compositions for taggingpolynucleotides and for identifying such tagged polynucleotides selectedfrom a mixture. Oligonucleotide tags comprising a plurality ofoligonucleotide subunits, or words, are attached to polynucleotides.Such tagged polynucleotides are then assayed in parallel, where one ormore tagged polynucleotides may be selected, for example, those havingparticular single nucleotide polymorphisms at one or more loci. Thepolynucleotides selected in the assay are then identified by analyzingtheir respective tags in accordance with the invention.

In one aspect, words of oligonucleotide tags index mixtures insuccessively more complex sets of mixtures (or “tiers” of mixtures, asdescribed more fully below) that a polynucleotide goes through in thetagging method of the invention. By identifying each word of anoligonucleotide tag, a sequence of submixtures is identified includingthe very first submixture that contains only a single polynucleotide,thereby providing the identity of the selected polynucleotide. Theanalysis of the words of an oligonucleotide tag can be carried out inparallel, e.g. by specific hybridization of the oligonucleotide tag toits tag complement on an addressable array; or such analysis may becarried out serially by successive specific hybridizations of labeledword complements, or by other serial processes described more fullybelow.

In one aspect, the invention provides a method of generating a mixtureof genomic fragments from a plurality of individuals wherein eachfragment from a different individual has a different oligonucleotide tagattached. Preferably, in this aspect, fragments from the same individualhave the same oligonucleotide tag attached. That is, each individual isassociated with a single unique oligonucleotide tag. In one aspect, suchmethod of generating a mixture of tagged polynucleotides is carried outwith the following steps: (a) providing a mutually discriminable setcontaining a plurality of words; (b) separately attaching a differentword to each of a plurality of different polynucleotides to formtag-polynucleotide conjugates, the plurality of differentpolynucleotides being equal to or less than the plurality of words; (c)repeating step (b) for each of the plurality of words to form a basetier of submixtures and recording which word is attached to eachpolynucleotide in each submixture; (d) combining tag-polynucleotideconjugates to form a tier of submixtures wherein each differentpolynucleotide within a submixture has an oligonucleotide tag that isdifferent from that of any other polynucleotide in the same submixture;(e) adding a different word to each different submixture of step (d) toform another tier of submixtures of tag-polynucleotide conjugates andrecording which word is attached to each tag-polynucleotide conjugate ineach submixture; and (f) repeating steps (d) and (e) until eachpolynucleotide has an oligonucleotide tag attached.

In another aspect of the invention, polynucleotides, such as DNAfragments from different genomes, are tagged with differentoligonucleotide tags that are concatenates of a plurality ofoligonucleotide subunits, wherein the subunits of the oligonucleotidetag identify in a position-dependent manner successively less complexsub-mixtures from which the DNA fragments were derived. In oneembodiment of this aspect, a polynucleotide is identified in a mixtureof such tagged polynucleotide by the following steps: (a) selecting atagged polynucleotide from a mixture of tagged polynucleotides assembledfrom one or more tiers of submixtures, at least one such tier being abase tier containing submixtures that each contain a singlepolynucleotide of known identity, each tagged polynucleotide of themixture comprising a polynucleotide attached to a concatenate ofoligonucleotide subunits such that each different polynucleotide has adifferent concatenate and each oligonucleotide subunit has a nucleotidesequence and a position within such concatenate, the position of theoligonucleotide subunit uniquely identifying a tier of submixtures andthe nucleotide sequence of the oligonucleotide subunit uniquelyidentifying a submixture within such tier of submixtures; and (b)determining the nucleotide sequence of each oligonucleotide subunit ateach position of the concatenate of the tagged polynucleotide todetermine a submixture within the base tier containing thepolynucleotide, thereby determining the identity of the polynucleotide.

In another aspect of the invention, compositions comprising sets ofoligonucleotide tags are provided that may be identified by successivelyidentifying words by specific hybridization of word complements. In oneembodiment of this aspect, such sets comprise a plurality ofoligonucleotides each having a length of at least eight nucleotides andeach comprising a concatenate of two or more subunits, wherein eachsubunit has a length of from 3 to 10 nucleotides and is selected fromthe same mutually discriminable set, and wherein each subunit within aconcatenate is different.

BRIEF DESCRIPTION OF THE DRAWINGS

FIGS. 1A-1B illustrate an oligonucleotide tag-polynucleotide conjugatewherein the oligonucleotide tag is a concatenate of a plurality ofwords.

FIGS. 2A-2B illustrate a procedure for attaching an oligonucleotide tagto a polynucleotide by attaching words one at a time.

FIGS. 3A-3B illustrate a procedure for decoding an oligonucleotide tagby successively hybridizing labeled word complements.

FIGS. 4A-4E lists melting temperatures of selected tags consisting offour words each having the comma-less property.

FIG. 5 illustrates tagging of polynucleotides by successive addition ofoligonucleotide subunits, or “words.”

DEFINITIONS

Terms and symbols of nucleic acid chemistry, biochemistry, genetics, andmolecular biology used herein follow those of standard treatises andtexts in the field, e.g. Kornberg and Baker, DNA Replication, SecondEdition (W.H. Freeman, New York, 1992); Lehninger, Biochemistry, SecondEdition (Worth Publishers, New York, 1975); Strachan and Read, HumanMolecular Genetics, Second Edition (Wiley-Liss, New York, 1999);Eckstein, editor, Oligonucleotides and Analogs: A Practical Approach(Oxford University Press, New York, 1991); Gait, editor, OligonucleotideSynthesis: A Practical Approach (IRL Press, Oxford, 1984); and the like.

“Addressable” in reference to tag complements means that the nucleotidesequence, or perhaps other physical or chemical characteristics, of anend-attached probe, such as a tag complement, can be determined from itsaddress, i.e. a one-to-one correspondence between the sequence or otherproperty of the end-attached probe and a spatial location on, orcharacteristic of, the solid phase support to which it is attached.Preferably, an address of a tag complement is a spatial location, e.g.the planar coordinates of a particular region containing copies of theend-attached probe. However, end-attached probes may be addressed inother ways too, e.g. by microparticle size, shape, color, frequency ofmicro-transponder, or the like, e.g. Chandler et al, PCT publication WO97/14028.

“Amplicon” means the product of a polynucleotide amplification reaction.That is, it is a population of polynucleotides, usually double stranded,that are replicated from one or more starting sequences. The one or morestarting sequences may be one or more copies of the same sequence, or itmay be a mixture of different sequences. Amplicons may be produced by avariety of amplification reactions whose products are multiplereplicates of one or more target nucleic acids. Generally, amplificationreactions producing amplicons are “template-driven” in that base pairingof reactants, either nucleotides or oligonucleotides, have complementsin a template polynucleotide that are required for the creation ofreaction products. In one aspect, template-driven reactions are primerextensions with a nucleic acid polymerase or oligonucleotide ligationswith a nucleic acid ligase. Such reactions include, but are not limitedto, polymerase chain reactions (PCRs), linear polymerase reactions,nucleic acid sequence-based amplification (NASBAs), rolling circleamplifications, and the like, disclosed in the following references thatare incorporated herein by reference: Mullis et al, U.S. Pat. Nos.4,683,195; 4,965,188; 4,683,202; 4,800,159 (PCR); Gelfand et al, U.S.Pat. No. 5,210,015 (real-time PCR with “taqman” probes); Wittwer et al,U.S. Pat. No. 6,174,670; Kacian et al, U.S. Pat. No. 5,399,491(“NASBA”); Lizardi, U.S. Pat. No. 5,854,033; Aono et al, Japanese patentpubl. JP 4-262799 (rolling circle amplification); and the like. In oneaspect, amplicons of the invention are produced by PCRs. Anamplification reaction may be a “real-time” amplification if a detectionchemistry is available that permits a reaction product to be measured asthe amplification reaction progresses, e.g. “real-time PCR” describedbelow, or “real-time NASBA” as described in Leone et al, Nucleic AcidsResearch, 26: 2150-2155 (1998), and like references. As used herein, theterm “amplifying” means performing an amplification reaction. A“reaction mixture” means a solution containing all the necessaryreactants for performing a reaction, which may include, but not belimited to, buffering agents to maintain pH at a selected level during areaction, salts, co-factors, scavengers, and the like.

“Complementary or substantially complementary” refers to thehybridization or base pairing or the formation of a duplex betweennucleotides or nucleic acids, such as, for instance, between the twostrands of a double stranded DNA molecule or between an oligonucleotideprimer and a primer binding site on a single stranded nucleic acid.Complementary nucleotides are, generally, A and T (or A and U), or C andG. Two single stranded RNA or DNA molecules are said to be substantiallycomplementary when the nucleotides of one strand, optimally aligned andcompared and with appropriate nucleotide insertions or deletions, pairwith at least about 80% of the nucleotides of the other strand, usuallyat least about 90% to 95%, and more preferably from about 98 to 100%.Alternatively, substantial complementarity exists when an RNA or DNAstrand will hybridize under selective hybridization conditions to itscomplement. Typically, selective hybridization will occur when there isat least about 65% complementary over a stretch of at least 14 to 25nucleotides, preferably at least about 75%, more preferably at leastabout 90% complementary. See, M. Kanehisa Nucleic Acids Res. 12:203(1984), incorporated herein by reference.

“Complexity” in reference to a nucleic acid sequence means the totallength of unique sequence in one or more polynucleotides, such aspolynucleotides in a population, e.g. a cDNA or genomic library, or in agenome. The complexity of a genome can be equivalent to or less than thelength of a single copy of the genome (i.e. the haploid sequence). Theconcept of nucleic acid complexity and its affect on assays is furtherdisclosed in the following references: Wetmur, Critical Reviews inBiochemistry and Molecular Biology, 26: 227-259 (1991); Britten andDavidson, chapter 1 in Hames et al, editors, Nucleic Acid Hybridization:A Practical Approach (IRL Press, Oxford, 1985).

“Duplex” means at least two oligonucleotides and/or polynucleotides thatare fully or partially complementary undergo Watson-Crick type basepairing among all or most of their nucleotides so that a stable complexis formed. The terms “annealing” and “hybridization” are usedinterchangeably to mean the formation of a stable duplex. “Perfectlymatched” in reference to a duplex means that the poly- oroligonucleotide strands making up the duplex form a double strandedstructure with one another such that every nucleotide in each strandundergoes Watson-Crick basepairing with a nucleotide in the otherstrand. The term “duplex” comprehends the pairing of nucleoside analogs,such as deoxyinosine, nucleosides with 2-aminopurine bases, PNAs, andthe like, that may be employed. A “mismatch” in a duplex between twooligonucleotides or polynucleotides means that a pair of nucleotides inthe duplex fails to undergo Watson-Crick bonding.

“Genetic locus,” or “locus” in reference to a genome or targetpolynucleotide, means a contiguous subregion or segment of the genome ortarget polynucleotide. As used herein, genetic locus, or locus, mayrefer to the position of a nucleotide, a gene, or a portion of a gene ina genome, including mitochondrial DNA, or it may refer to any contiguousportion of genomic sequence whether or not it is within, or associatedwith, a gene. In one aspect, a genetic locus refers to any portion ofgenomic sequence, including mitochondrial DNA, from a single nucleotideto a segment of few hundred nucleotides, e.g. 100-300, in length.

“Genetic variant” means a substitution, inversion, insertion, ordeletion of one or more nucleotides at genetic locus, or a translocationof DNA from one genetic locus to another genetic locus. In one aspect,genetic variant means an alternative nucleotide sequence at a geneticlocus that may be present in a population of individuals and thatincludes nucleotide substitutions, insertions, and deletions withrespect to other members of the population. In another aspect,insertions or deletions at a genetic locus comprises the addition or theabsence of from 1 to 10 nucleotides at such locus, in comparison withthe same locus in another individual of a population.

“Kit” refers to any delivery system for delivering materials or reagentsfor carrying out a method of the invention. In the context of reactionassays, such delivery systems include systems that allow for thestorage, transport, or delivery of reaction reagents (e.g., probes,enzymes, etc. in the appropriate containers) and/or supporting materials(e.g., buffers, written instructions for performing the assay etc.) fromone location to another. For example, kits include one or moreenclosures (e.g., boxes) containing the relevant reaction reagentsand/or supporting materials. Such contents may be delivered to theintended recipient together or separately. For example, a firstcontainer may contain an enzyme for use in an assay, while a secondcontainer contains probes.

“Ligation” means to form a covalent bond or linkage between the terminiof two or more nucleic acids, e.g. oligonucleotides and/orpolynucleotides, in a template-driven reaction. The nature of the bondor linkage may vary widely and the ligation may be carried outenzymatically or chemically. As used herein, ligations are usuallycarried out enzymatically to form a phosphodiester linkage between a 5′carbon of a terminal nucleotide of one oligonucleotide with 3′ carbon ofanother oligonucleotide. A variety of template-driven ligation reactionsare described in the following references, which are incorporated byreference: Whitely et al, U.S. Pat. No. 4,883,750; Letsinger et al, U.S.Pat. No. 5,476,930; Fung et al, U.S. Pat. No. 5,593,826; Kool, U.S. Pat.No. 5,426,180; Landegren et al, U.S. Pat. No. 5,871,921; Xu and Kool,Nucleic Acids Research, 27: 875-881 (1999); Higgins et al, Methods inEnzymology, 68: 50-71 (1979); Engler et al, The Enzymes, 15: 3-29(1982); and Namsaraev, U.S. patent publication 2004/0110213.

“Microarray” refers to a solid phase support having a planar surface,which carries an array of nucleic acids, each member of the arraycomprising identical copies of an oligonucleotide or polynucleotideimmobilized to a spatially defined region or site, which does notoverlap with those of other members of the array; that is, the regionsor sites are spatially discrete. Spatially defined hybridization sitesmay additionally be “addressable” in that its location and the identityof its immobilized oligonucleotide are known or predetermined, forexample, prior to its use. Typically, the oligonucleotides orpolynucleotides are single stranded and are covalently attached to thesolid phase support, usually by a 5′-end or a 3′-end. The density ofnon-overlapping regions containing nucleic acids in a microarray istypically greater than 100 per cm², and more preferably, greater than1000 per cm². Microarray technology is reviewed in the followingreferences: Schena, Editor, Microarrays: A Practical Approach (IRLPress, Oxford, 2000); Southern, Current Opin. Chem. Biol., 2: 404-410(1998); Nature Genetics Supplement, 21: 1-60 (1999). As used herein,“random microarray” refers to a microarray whose spatially discreteregions of oligonucleotides or polynucleotides are not spatiallyaddressed. That is, the identity of the attached oligonucleoties orpolynucleotides is not discernable, at least initially, from itslocation. In one aspect, random microarrays are planar arrays ofmicrobeads wherein each microbead has attached a single kind ofhybridization tag complement, such as from a minimally cross-hybridizingset of oligonucleotides. Arrays of microbeads may be formed in a varietyof ways, e.g. Brenner et al, Nature Biotechnology, 18: 630-634 (2000);Tulley et al, U.S. Pat. No. 6,133,043; Stuelpnagel et al, U.S. Pat. No.6,396,995; Chee et al, U.S. Pat. No. 6,544,732; and the like. Likewise,after formation, microbeads, or oligonucleotides thereof, in a randomarray may be identified in a variety of ways, including by opticallabels, e.g. fluorescent dye ratios or quantum dots, shape, sequenceanalysis, or the like.

“Nucleoside” as used herein includes the natural nucleosides, including2′-deoxy and 2′-hydroxyl forms, e.g. as described in Kornberg and Baker,DNA Replication, 2nd Ed. (Freeman, San Francisco, 1992). “Analogs” inreference to nucleosides includes synthetic nucleosides having modifiedbase moieties and/or modified sugar moieties, e.g. described by Scheit,Nucleotide Analogs (John Wiley, New York, 1980); Uhlman and Peyman,Chemical Reviews, 90: 543-584 (1990), or the like, with the proviso thatthey are capable of specific hybridization. Such analogs includesynthetic nucleosides designed to enhance binding properties, reducecomplexity, increase specificity, and the like. Polynucleotidescomprising analogs with enhanced hybridization or nuclease resistanceproperties are described in Uhlman and Peyman (cited above); Crooke etal, Exp. Opin. Ther. Patents, 6: 855-870 (1996); Mesmaeker et al,Current Opinion in Structual Biology, 5: 343-355 (1995); and the like.Exemplary types of polynucleotides that are capable of enhancing duplexstability include oligonucleotide N3′→P5′ phosphoramidates (referred toherein as “amidates”), peptide nucleic acids (referred to herein as“PNAs”), oligo-2′-O-alkylribonucleotides, polynucleotides containing C-5propynylpyrimidines, locked nucleic acids (LNAs), and like compounds.Such oligonucleotides are either available commercially or may besynthesized using methods described in the literature.

“Oligonucleotide tag” means an oligonucleotide that is attached to apolynucleotide and is used to identify and/or track the polynucleotidein a reaction. Usually, a oligonucleotide tag is attached to the 3′- or5′-end of a polynucleotide to form a linear conjugate, sometime referredto herein as a “tagged polynucleotide,” or equivalently, an“oligonucleotide tag-polynucleotide conjugate,” or “tag-polynucleotideconjugate.” Oligonucleotide tags may vary widely in size andcompositions; the following references provide guidance for selectingsets of oligonucleotide tags appropriate for particular embodiments:Brenner, U.S. Pat. No. 5,635,400; Brenner et al, Proc. Natl. Acad. Sci.,97: 1665-1670 (2000); Shoemaker et al, Nature Genetics, 14: 450-456(1996); Morris et al, European patent publication 0799897A1; Wallace,U.S. Pat. No. 5,981,179; and the like. In different applications of theinvention, oligonucleotide tags can each have a length within a range offrom 4 to 36 nucleotides, or from 6 to 30 nucleotides, or from 8 to 20nucleotides, respectively. In one aspect, oligonucleotide tags are usedin sets, or repertoires, wherein each oligonucleotide tag of the set hasa unique nucleotide sequence. In some embodiment, particularly whereoligonucleotide tags are used to sort polynucleotides, or where they areidentified by specific hybridization, each oligonucleotide tag of such aset has a melting temperature that is substantially the same as that ofevery other member of the same set. In such aspects, the meltingtemperatures of oligonucleotide tags within a set are within 10° C. ofone another; in another embodiment, they are within 5° C. of oneanother; and in another embodiment, they are within 2° C. of oneanother. In another aspect, oligonucleotide tags are members of amutually discriminable set, as described more fully below. The size ofmutually discriminable sets of oligonucleotide tags may vary widely.Such a set of oligonucleotide tags may have a size in the range of fromseveral tens to many thousands, or even millions, e.g. 50 to 1.6×10⁶. Inanother embodiment, such a size is in the range of from 200 to 40,000;or from 1000 to 40,000; or from 1000 to 10,000. In another aspect of theinvention, oligonucletide tags comprise a concatenation of subunits,such as described by Brenner et al, Proc. Natl. Acad. Sci., 97:1665-1670 (2000). In such concatenates, oligonucleotide subunits, orwords, can be selected from a set of subunits with the properties ofmutual discriminability and substantially equivalent meltingtemperature. Constructing oligonucleotide tags from a plurality ofoligonucleotide subunits permits the convenient and inexpensiveformation of very large sets of oligonucleotide tags, e.g. as describedby Brenner et al, Proc. Natl. Acad. Sci., 97: 1665-1670 (2000). Also,the use of oligonucleotide subunits permits enzymatic synthesis and/orattachment of oligonucleotide tags to polynucleotides, e.g. as describedbelow and in Brenner and Williams, U.S. patent publication 2003/0049616.In one aspect, oligonucleotide tags comprise a plurality ofoligonucleotide subunits. Such subunits may vary widely in length. Inone aspect, the length of oligonucleotide subunits is in the range offrom 2 to 18 nucleotides; in another aspect, the length ofoligonucleotide subunits is in the range of from 2 to 8 nucleotides; andin another aspect the length of oligonucleotide subunits is in the rangeof from 2 to 5 nucleotides. A plurality of oligonucleotide subunitsmaking up an oligonucleotide tag may also vary widely depending on theirapplication. In one aspect, such plurality is a number in the range of 2to 10; and in another aspect, such plurality is a number in the range offrom 2 to 6. The size of a set of oligonucleotide subunits is usuallysmaller than the size of a set of oligonucleotide tags. Usually, a setof oligonucleotide subunits has a size in the range of from 2 to 20; orin another embodiment, from 2 to 10; or in another embodiment, from 4 to8. It is clear to one of ordinary skill that for subunits only twonucleotides in length that the size of a set of subunits would besmaller than that of subunits having greater lengths.

“Polymerase chain reaction,” or “PCR,” means a reaction for the in vitroamplification of specific DNA sequences by the simultaneous primerextension of complementary strands of DNA. In other words, PCR is areaction for making multiple copies or replicates of a target nucleicacid flanked by primer binding sites, such reaction comprising one ormore repetitions of the following steps: (i) denaturing the targetnucleic acid, (ii) annealing primers to the primer binding sites, and(iii) extending the primers by a nucleic acid polymerase in the presenceof nucleoside triphosphates. Usually, the reaction is cycled throughdifferent temperatures optimized for each step in a thermal cyclerinstrument. Particular temperatures, durations at each step, and ratesof change between steps depend on many factors well-known to those ofordinary skill in the art, e.g. exemplified by the references: McPhersonet al, editors, PCR: A Practical Approach and PCR2: A Practical Approach(IRL Press, Oxford, 1991 and 1995, respectively). For example, in aconventional PCR using Taq DNA polymerase, a double stranded targetnucleic acid may be denatured at a temperature >90° C., primers annealedat a temperature in the range 50-75° C., and primers extended at atemperature in the range 72-78° C. The term “PCR” encompasses derivativeforms of the reaction, including but not limited to, RT-PCR, real-timePCR, nested PCR, quantitative PCR, multiplexed PCR, and the like.Reaction volumes range from a few hundred nanoliters, e.g. 200 nL, to afew hundred μL, e.g. 200 μL. “Reverse transcription PCR,” or “RT-PCR,”means a PCR that is preceded by a reverse transcription reaction thatconverts a target RNA to a complementary single stranded DNA, which isthen amplified, e.g. Tecott et al, U.S. Pat. No. 5,168,038, which patentis incorporated herein by reference. “Real-time PCR” means a PCR forwhich the amount of reaction product, i.e. amplicon, is monitored as thereaction proceeds. There are many forms of real-time PCR that differmainly in the detection chemistries used for monitoring the reactionproduct, e.g. Gelfand et al, U.S. Pat. No. 5,210,015 (“taqman”); Wittweret al, U.S. Pat. Nos. 6,174,670 and 6,569,627 (intercalating dyes);Tyagi et al, U.S. Pat. No. 5,925,517 (molecular beacons); which patentsare incorporated herein by reference. Detection chemistries forreal-time PCR are reviewed in Mackay et al, Nucleic Acids Research, 30:1292-1305 (2002), which is also incorporated herein by reference.“Nested PCR” means a two-stage PCR wherein the amplicon of a first PCRbecomes the sample for a second PCR using a new set of primers, at leastone of which binds to an interior location of the first amplicon. Asused herein, “initial primers” in reference to a nested amplificationreaction mean the primers used to generate a first amplicon, and“secondary primers” mean the one or more primers used to generate asecond, or nested, amplicon. “Multiplexed PCR” means a PCR whereinmultiple target sequences (or a single target sequence and one or morereference sequences) are simultaneously carried out in the same reactionmixture, e.g. Bernard et al, Anal. Biochem., 273: 221-228(1999)(two-color real-time PCR). Usually, distinct sets of primers areemployed for each sequence being amplified. “Quantitative PCR” means aPCR designed to measure the abundance of one or more specific targetsequences in a sample or specimen. Quantitative PCR includes bothabsolute quantitation and relative quantitation of such targetsequences. Quantitative measurements are made using one or morereference sequences that may be assayed separately or together with atarget sequence. The reference sequence may be endogenous or exogenousto a sample or specimen, and in the latter case, may comprise one ormore competitor templates. Typical endogenous reference sequencesinclude segments of transcripts of the following genes: β-actin, GAPDH,β₂-microglobulin, ribosomal RNA, and the like. Techniques forquantitative PCR are well-known to those of ordinary skill in the art,as exemplified in the following references that are incorporated byreference: Freeman et al, Biotechniques, 26: 112-126 (1999);Becker-Andre et al, Nucleic Acids Research, 17: 9437-9447 (1989);Zimmerman et al, Biotechniques, 21: 268-279 (1996); Diviacco et al,Gene, 122: 3013-3020 (1992); Becker-Andre et al, Nucleic Acids Research,17: 9437-9446 (1989); and the like.

“Polynucleotide” or “oligonucleotide” are used interchangeably and eachmean a linear polymer of nucleotide monomers. Monomers making uppolynucleotides and oligonucleotides are capable of specifically bindingto a natural polynucleotide by way of a regular pattern ofmonomer-to-monomer interactions, such as Watson-Crick type of basepairing, base stacking, Hoogsteen or reverse Hoogsteen types of basepairing, or the like. Such monomers and their internucleosidic linkagesmay be naturally occurring or may be analogs thereof, e.g. naturallyoccurring or non-naturally occurring analogs. Non-naturally occurringanalogs may include PNAs, phosphorothioate internucleosidic linkages,bases containing linking groups permitting the attachment of labels,such as fluorophores, or haptens, and the like. Whenever the use of anoligonucleotide or polynucleotide requires enzymatic processing, such asextension by a polymerase, ligation by a ligase, or the like, one ofordinary skill would understand that oligonucleotides or polynucleotidesin those instances would not contain certain analogs of internucleosidiclinkages, sugar moities, or bases at any or some positions.Polynucleotides typically range in size from a few monomeric units, e.g.5-40, when they are usually referred to as “oligonucleotides,” toseveral thousand monomeric units. Whenever a polynucleotide oroligonucleotide is represented by a sequence of letters (upper or lowercase), such as “ATGCCTG,” it will be understood that the nucleotides arein 5′→3′ order from left to right and that “A” denotes deoxyadenosine,“C” denotes deoxycytidine, “G” denotes deoxyguanosine, and “T” denotesthymidine, “I” denotes deoxyinosine, “U” denotes uridine, unlessotherwise indicated or obvious from context. Unless otherwise noted theterminology and atom numbering conventions will follow those disclosedin Strachan and Read, Human Molecular Genetics 2 (Wiley-Liss, New York,1999). Usually polynucleotides comprise the four natural nucleosides(e.g. deoxyadenosine, deoxycytidine, deoxyguanosine, deoxythymidine forDNA or their ribose counterparts for RNA) linked by phosphodiesterlinkages; however, they may also comprise non-natural nucleotideanalogs, e.g. including modified bases, sugars, or internucleosidiclinkages. It is clear to those skilled in the art that where an enzymehas specific oligonucleotide or polynucleotide substrate requirementsfor activity, e.g. single stranded DNA, RNA/DNA duplex, or the like,then selection of appropriate composition for the oligonucleotide orpolynucleotide substrates is well within the knowledge of one ofordinary skill, especially with guidance from treatises, such asSambrook et al, Molecular Cloning, Second Edition (Cold Spring HarborLaboratory, New York, 1989), and like references.

“Primer” means an oligonucleotide, either natural or synthetic, that iscapable, upon forming a duplex with a polynucleotide template, of actingas a point of initiation of nucleic acid synthesis and being extendedfrom its 3′ end along the template so that an extended duplex is formed.The sequence of nucleotides added during the extension process aredetermined by the sequence of the template polynucleotide. Usuallyprimers are extended by a DNA polymerase. Primers usually have a lengthin the range of from 14 to 36 nucleotides.

“Readout” means a parameter, or parameters, which are measured and/ordetected that can be converted to a number or value. In some contexts,readout may refer to an actual numerical representation of suchcollected or recorded data. For example, a readout of fluorescentintensity signals from a microarray is the address and fluorescenceintensity of a signal being generated at each hybridization site of themicroarray; thus, such a readout may be registered or stored in variousways, for example, as an image of the microarray, as a table of numbers,or the like.

“Solid support”, “support”, and “solid phase support” are usedinterchangeably and refer to a material or group of materials having arigid or semi-rigid surface or surfaces. In many embodiments, at leastone surface of the solid support will be substantially flat, although insome embodiments it may be desirable to physically separate synthesisregions for different compounds with, for example, wells, raisedregions, pins, etched trenches, or the like. According to otherembodiments, the solid support(s) will take the form of beads, resins,gels, microspheres, or other geometric configurations. Microarraysusually comprise at least one planar solid phase support, such as aglass microscope slide.

“Specific” or “specificity” in reference to the binding of one moleculeto another molecule, such as a labeled target sequence for a probe,means the recognition, contact, and formation of a stable complexbetween the two molecules, together with substantially less recognition,contact, or complex formation of that molecule with other molecules. Inone aspect, “specific” in reference to the binding of a first moleculeto a second molecule means that to the extent the first moleculerecognizes and forms a complex with another molecules in a reaction orsample, it forms the largest number of the complexes with the secondmolecule. Preferably, this largest number is at least fifty percent.Generally, molecules involved in a specific binding event have areas ontheir surfaces or in cavities giving rise to specific recognitionbetween the molecules binding to each other. Examples of specificbinding include antibody-antigen interactions, enzyme-substrateinteractions, formation of duplexes or triplexes among polynucleotidesand/or oligonucleotides, receptor-ligand interactions, and the like. Asused herein, “contact” in reference to specificity or specific bindingmeans two molecules are close enough that weak noncovalent chemicalinteractions, such as Van der Waal forces, hydrogen bonding,base-stacking interactions, ionic and hydrophobic interactions, and thelike, dominate the interaction of the molecules.

“T_(m),” or “melting temperature” is the temperature at which apopulation of double-stranded nucleic acid molecules becomes halfdissociated into single strands. Several equations for calculating theTm of nucleic acids are well known in the art. As indicated by standardreferences, a simple estimate of the Tm value may be calculated by theequation. T_(m)=81.5+0.41 (% G+C), when a nucleic acid is in aqueoussolution at 1 M NaCl (see e.g., Anderson and Young, Quantitative FilterHybridization, in Nucleic Acid Hybridization (1985). Other references(e.g., Allawi, H. T. & SantaLucia, J., Jr., Biochemistry 36, 10581-94(1997)) include alternative methods of computation which take structuraland environmental, as well as sequence characteristics into account forthe calculation of Tm.

“Sample” means a quantity of material from a biological, environmental,medical, or patient source in which detection or measurement of targetnucleic acids is sought. On the one hand it is meant to include aspecimen or culture (e.g., microbiological cultures). On the other hand,it is meant to include both biological and environmental samples. Asample may include a specimen of synthetic origin. Biological samplesmay be animal, including human, fluid, solid (e.g., stool) or tissue, aswell as liquid and solid food and feed products and ingredients such asdairy items, vegetables, meat and meat by-products, and waste.Biological samples may include materials taken from a patient including,but not limited to cultures, blood, saliva, cerebral spinal fluid,pleural fluid, milk, lymph, sputum, semen, needle aspirates, and thelike. Biological samples may be obtained from all of the variousfamilies of domestic animals, as well as feral or wild animals,including, but not limited to, such animals as ungulates, bear, fish,rodents, etc. Environmental samples include environmental material suchas surface matter, soil, water and industrial samples, as well assamples obtained from food and dairy processing instruments, apparatus,equipment, utensils, disposable and non-disposable items. These examplesare not to be construed as limiting the sample types applicable to thepresent invention.

DETAILED DESCRIPTION OF THE INVENTION

The invention provides methods and compositions for attachingoligonucleotide tags to polynucleotides for the purpose of carrying outanalytical assays in parallel and for decoding the oligonucleotide tagsof polynucleotides selected in such assays. Exemplary analytical assayswhere tagged polynucleotides are selected include genotyping assays,such as disclosed in the following references that are incorporated byreferences: Brenner, PCT patent publication WO 2005/026686; Willis etal, U.S. Pat. No. 6,858,412; Fan et al, U.S. patent publication2005/0074787; Schouten, U.S. patent publication 2003/0108913; and thelike. Selection of a tagged polynucleotide may be based on specifichybridization and differential duplex stability, template-drivenligation, template-driven strand extension, exonuclease digestion (e.g.of non-circularized probes), or the like.

In one aspect, as illustrated in FIG. 1A, oligonucleotide tags (100) ofthe invention are concatenates of a plurality of oligonucleotidesubunits, or words (e.g., labeled t₁, t₂, t₃, . . . t_(k) in FIG. 1A)that can be attached to polynucleotide (102) to form a linear conjugate.In another aspect of the invention, words are added to polynucleotidesin a succession of mixtures, each one more complex than the previousone. (Thus, in the embodiment illustrated below, each added wordprovides an address of a successively more complex submixture, inanalogy to a geographical progression: house, street, district, city,state, country, and so on). That is, as illustrated in FIG. 1B, whereeach dot represents a vessel or well (e.g. in a 384-well plate, or likeapparatus) containing a single kind of polynucleotide, each differentkind of polynucleotide in each 4×4 subgroup has a different two wordspair attached that provide a unique address for each polynucleotide inthe 4×4 subgroup. In this example, such addresses are provided by wordsfrom a mutually discriminable set of words having at least four members.For larger starting subgroups, e.g. 8×8 as disclosed below, larger setsof words are required. Thus, in FIG. 1B, words r₃ and c₁ give theaddress of polynucleotide (102) within subgroup (108), the locationbeing indicated by circle (109). Words C₂ and R₂ give the address ofsubgroup (108) within a quadrant, and word Q₁ indicates the quadrant inwhich subgroup (108) is located.

A method of attaching oligonucleotide tags of the invention topolynucleotides is illustrated in FIGS. 2A-2B. Polynucleotides (200) aregenerated that have overhanging ends (202), for example, by digesting asample, such as genomic DNA, cDNA, or the like, with a restrictionendonuclease. Preferably, a restriction endonuclease is used that leavesa four-base 5′ overhang that can be filled-in by one nucleotide torender the fragments incapable of self-ligation. For example, digestionwith Bgl II followed by an extension with a DNA polymerase in thepresence of dGTP produces such ends. Next, to such fragments,single-word adaptors (206) are ligated (204). Single-word adaptors (206)(i) attach a first word of an oligonucleotide tag to both ends of eachfragment (200). Single-word adaptors (206) also contain a recognitionsite for a type IIs restriction endonuclease that preferably leaves a 5′four base overhang and that is positioned so that its cleavage sitecorresponds to the position of the newly added word, as described morefully in the examples below. (Such cleavage allows words to be addedone-by-one by use of a set of adaptors containind word pairs, or“di-words,” described more fully below). In one aspect, a single-wordadaptor (206) is separately ligated to fragments (200) from eachdifferent individual genome.

In order to carry out enzymatic operations at only one end of adaptoredfragments (205), one of the two ends of each fragment is protected bymethylation and operations are carried out with enzymes sensitive to5-methyldeoxycytidine in their recognition sites. Adaptored fragments(205) are melted (208) after which primer (210) is annealed as shown andextended by a DNA polymerase in the presence of 5-methyldeoxycytidinetriphosphate and the other dNTPs to give hemi-methylated polynucleotide(212). Polynucleotides (212) are then digested with a restrictionendonuclease that is blocked by a methylated recognition site, e.g. DpnII (which cleaves at a recognition site internal to the Bgl II site andleaves the same overhang). Accordingly, such restriction endonucleasesmust have a deoxycytidine in its recognition sequence and leave anoverhanging end to facilitate the subsequent ligation of adaptors.Digestion leaves fragment (212) with overhang (216) at only one end andfree biotinylated fragments (213). After removal (218) of biotinylatedfragments (213) (for example by affinity capture with avidinated beads),adaptor (220) may be ligated to fragment (212) in order to introducesequence elements, such as primer binding sites, for an analyticaloperation, such as sequencing, SNP detection, or the like. Such adaptoris conveniently biotinylated for capture onto a solid phase support sothat repeated cycles of ligation, cleavage, and washing can beimplemented for attaching words of the oligonucleotide tags. Afterligation of adaptor (220), a portion of single-word adaptor (224) iscleaved so that overhang (226) is created that includes all (orsubstantially all, e.g. 4 out of 5 bases of) the single word added bysingle-word adaptor (206). After washing to remove fragment (224), aplurality of cycles (232) are carried out in which adaptors (230)containing di-words are successively ligated (234) to fragment (231) andcleaved (235) to leave an additional word. Such cycles are continueduntil the oligonucleotide tags (240) are complete, after which thetagged polynucleotides may be subjected to analysis directly, or singlestrands thereof may be melted from the solid phase support for analysis.

Non-Sequential Decoding

In some tagging schemes, words may be repeated within an oligonucleotidetag. For example, where all words are selected from the same mutuallydiscriminable set “with replacement” (i.e. at each word position withina concatenate, any word of a set can be added), then repeated words arepossible. In such embodiments, oligonucleotide tags can be decoded (thatis, its associated polynucleotide can be identified) in a number ofways. In one aspect, labeled copies of oligonucleotide tags can bespecifically hybridized to their tag complements on an addressablemicroarray, or like readout platform. Alternatively, particularly in thecase of ligation tags, the oligonucleotide tags can be translated into adifferent kind of tag that permits a particular type of readout. Forexample, ligation tags can be specifically hybridized directly to amicroarray of tag complements (preferably, comprising oligonucleotideanalogs such as PNAs that have enhanced binding energy per basepair) orligation tags can be specifically hybridized indirectly to a microarrayof tag complements by first translating them into a hybridization tagsof greater length. Ligation tags also can be translated into size-codedtags that can be identified by separating by electrophoresis. The formerdecoding is carried out using the tag translation methods disclosed inBrenner, PCT patent publication WO 2005/026686, which is incorporatedherein by reference. The latter decoding is carried out using the tagtranslation method disclosed in Brenner, U.S. provisional patent Ser.No. 60/662,167, which is incorporated herein by reference.

Sequential Decoding

In tagging schemes where there are no repeated words in anoligonucleotide tag (as disclosed below), in addition to paralleldecoding, such as specific hybridization of the entire oligonucleotidetags to their respective tag complements, such oligonucleotide tags canbe decoded sequentially by word-by-word identification. As illustratedin FIG. 3A, tagged polynucleotide (302) has oligonucleotide tag (300)that does not contain repeated words. Such polynucleotide is captured(304) onto a solid phase support (306), using conventional protocols,e.g. avidin or streptavidin capture via a biotin moiety. Labeledanti-word (310) is then specifically hybridized to its correspondingword in the oligonucleotide tag and detected via a fluorescent label, orlike label, after which it is melted (312) and the next anti-word (316)is specifically hybridized (314). The process is repeated until all ofthe words are identified. In some embodiments, as illustrated in FIG.3B, anti-words (350) may include a segment that is complementary to aspacer segment (352) adjacent and between words, e.g. W₁, W₂, and W₃.

Ligation Tags

In one aspect, oligonucleotides of the invention include tags thatachieve discrimination both by sequence differences and by ligation.These are referred to herein as “ligation tags.” In one aspect, ends ofligation tags are correlated in that if one end matches, which isrequired for ligation, the other end matches as well. The sequences alsoallow the use of a special set of enzymes whih can create overhangs of(for example) eight bases required for a set of 4096 differentsequences. In one aspect, ligation tags of a set each have a length inthe range of from 6 to 12 nucleotides, and more preferably, from 8 to 10nucleotides. In one aspect, a set of ligation tags is selected so thateach member of a set differs from every other member of the same set byat least one nucleotide. In the following disclosure, it is assume thata starting DNA is obtainable having the following form:

where L is a sequence to the “left” of the template that may bepreselected, and R1 and R2 are primer binding sites (to the “right” ofthe template) In one aspect, nucleotide sequences of ligation tags in aset, i.e. ligation codes, may be defined by the following formula:

5′-Y[NN]Z[NN]Y

where Y is A, C, G, or T; N is any nucleotide; and Z is (5′→3′) GT, TG,CA, or AC. The central doublet, Z, is there there so that restrictionenzymes can be used to create the overhangs. Note ends of the tags arecorrelated, so if one does not ligate, the other will not either. Thus,the ends and the middle pair differ by 2 bases out of 8 from nearestneighbors, i.e. 25%, whereas the inners differ by one base in 8, i.e.12.5%. Note that the above code may be expanded to give over 16,000 tagsby adding an additional doublet, as in the formula: 5′-Y[NN]ZZ[NN]Y,where each Z is independently selected from the set of doublets.

In order to create an overhang of bases, a combination of a nickingenzyme and a type Hs restriction endonuclease having a cleavage siteoutside of its recognition site is used. Preferably, such type I isrestriction endonuclease leaves a 5′ overhang. Such enzymes are selectedalong with the set of doublets, Z, to exclude such sites from theligation code. In one aspect, the following enzymes may be used with theabove code: Nicking enzyme: N.Alw I (GGATCN₄↓); Restriction enzyme: FauI (CCCGC(N₄/N₆)). Sap I (GCTCTTC(N₁/N₄)) may also be used as arestriction enzyme. In one example, these enzymes are used with thefollowing segments:

Enzyme Sequence N.Alw I GGATC[TTCT]↓ Fau I CCCGC[TTCT]↓ Sap IGCTCTTC[T]↓A 5′ overhang can be created as follows, if a ligation code, designatedas “[LIG8],” is present (SEQ ID NO: 1):

When this structure is cleaved as shown above, two double-strandedpieces are formed (SEQ ID NO: 2):

5′ . . . GGATCTTCT pNNAGAAGCGGG . . . 3′ 3′ . . . CCTAGAAGA[LIG8]p   TCTTCGCCC . . . 5′where “p” represents a phosphate group.

As described above, the doublet code, Z, consisted of TG, GT, AC, andCA. These differ from each other by two mismatches and a 5 word sequenceproviding 1000 different sequences has a discrimination of 2 bases in10. Another way to consider such a doublet structure is to definesymbols c=G or G, a=A or T. The above code can then be expressed as ca,aa, cc, and ac. ca has the dinucleotides CA, CT, GA, and GT. Notice thatin this set, each “word” differs by 1 mismatch from 2 members of the setbut by 2 mismatches from the remaining members. The doublet code ispresent by definition. In fact, it is easy to see that if another repeatstructure is selected, for example, caca, then many words would be foundthat differ by two mismatches. The c and a pairs may be arranged in anymanner. For example, a sequence defining a set of 256 members could be,cacacaca, which has a clearly defined substructure, or acaaccca, whichhas no repeated segments. Both have 50% GC and neither has sequencesthat are self complementary, but the following sequence does: cacaacac.

It is well known that the melting and annealing behavior of DNAsequences depends not only on the amount GC, but more strongly on theneighboring base. Thus, cc pairs GG, CC, CG, GC contribute most toduplex stability, while ca and ac pairs make the same but lowercontribution and, of the aa pairs TA is lower than the remaining threeAT, AA and TT, which are like the ca and ac set. The weakness of thedoublet code is that the junctions between the doublets generate caseswhere there are GG in one sequence and TA in another at the same place.This cannot happen with the binary code chosen above no matter how theunits are arranged. Thus, cc would be uniformly high and the aa low butwith the pair TA being lower than the others. Another binary system,e.g. t=G or T, or A, would have a different neighbor structure in whichthere would be GC and TA at the same place.

It is desirable that this criterion be extended to the neighbors of theouter correlated nucleotides, which can be accomplished by requiring asequence that begins with an a and ends with an a. A code for the inner8 bases which satisfies these conditions is the following (SEQ ID NO:3):

5′-Y′accacacaY″

where Y′ is G, A, T, or C, and Y″ is T whenever Y′ is G, C whenever Y′is A, G whenever Y′ is T, and A whenever Y′ is C.

Direct Readout of Ligation Tags

In one aspect, after an analytical operation is conducted in which tagsare selected and labeled, such tags may be detected on an array, ormicroarray, of tag complements, as shown below. Selected ligation tagsmay be in an amplifiable segment as follows (SEQ ID NO: 4):

Cleavage of this structure gives the following, the upper strand ofwhich may be labeled, e.g. with a fluorescent dye, quantum dot, hapten,or the like, using conventional techniques:

5′ [Primer L]GGATCNNNN 3′ [Primer L]CCTAGNNNN[LIG8]p-5′This fragment may be hybridized to an array of tag complements such asthe following:

where the oligonucleotide designated as “10” may be added before or withthe labeled ligation tag.

After a hybridization reaction, hybridized ligation tags are ligated tooligonucleotide “10” to ensure that a stable structure is formed. Theends between the upper Primer L and the tag complement are not ligatedbecause of the absence of a 5′ phosphate on the tag complement. Such anarrangement permits the washing and re-use of the solid phase support.In one aspect, tag complements and the other components attached to thesolid phase support are peptide nucleic acids (PNAs) to facilitate suchre-use.

Hybridization Tags

A feature of the invention is the use of oligonucleotide tags touniquely label members of a population of polynucleotides. A widevariety of oligonucleotide tags may be employed for this purpose. In oneaspect, oligonucleotide tags are selected from the same set ofoligonucleotides that have nucleotide sequences that render themmutually discriminable. That is, annealing conditions, or hybridizationconditions, are available so that an oligonucleotide tag of a set formsa stable duplex with essentially only its complement and not with thecomplements of any other oligonucleotide tag of the same set. A set ofmutually discriminable oligonucleotide tags can vary widely in sequence,length, and internal structure. In one aspect, each oligonucleotide tagof such a set differs in sequence from every other member of the sameset in at least ten percent of its nucleotide positions or each isselected from a minimally cross-hybridizing set of oligonucleotides. Inanother aspect, each oligonucleotide tag of such a set differs insequence from every other member of the same set in at least fifteenpercent of its nucleotide positions or each is selected from a minimallycross-hybridizing set of oligonucleotides. Thus, in the latter example,a set of 6-mer oligonucleotides whose members each differ from oneanother by at least one nucleotide form a mutually discriminable set.

In another aspect, mutually discriminable oligonucleotide tags areselected solely from a minimally cross-hybridizing set ofoligonucleotides, or assembled from oligonucleotide subunits, i.e.“words,” selected from a minimally cross-hybridizing set ofoligonucleotides. Construction of such minimally cross-hybridizing setsare disclosed in Brenner et al, U.S. Pat. No. 5,846,719; Brenner et al,Proc. Natl. Acad. Sci., 97: 1665-1670 (2000); and Brenner and Williams,U.S. patent publication 2003/0049616, which references are incorporatedby reference. In accordance with Brenner, the sequences ofoligonucleotides of a minimally cross-hybridizing set differ from thesequences of every other member of the same set by at least twonucleotides. Thus, each member of such a set cannot form a duplex (ortriplex) with the complement of any other member with less than twomismatches. Preferably, perfectly matched duplexes of tags and tagcomplements of either the same mutually discriminable set or the sameminimally cross-hybridizing set have approximately the same stability,especially as measured by melting temperature and/or dissociationtemperature. Complements of hybridization tags, referred to herein as“tag complements,” may comprise natural nucleotides or non-naturalnucleotide analogs. Hybridization tags when used with theircorresponding tag complements provide a means of enhancing thespecificity, or discrimination, of hybridization.

Minimally cross-hybridizing sets of oligonucleotide tags and tagcomplements may be synthesized either combinatorially or individuallydepending on the size of the set desired and the degree to whichcross-hybridization is sought to be minimized (or stated another way,the degree to which specificity is sought to be enhanced). For example,a minimally cross-hybridizing set may consist of a set of individuallysynthesized 10-mer sequences that differ from each other by at least 4nucleotides, such set having a maximum size of 332, when constructed asdisclosed in Brenner et al, International patent applicationPCT/US96/09513. Alternatively, a minimally cross-hybridizing set ofoligonucleotide tags may also be assembled combinatorially from subunitswhich themselves are selected from a minimally cross-hybridizing set.For example, a set of minimally cross-hybridizing 12-mers differing fromone another by at least three nucleotides may be synthesized byassembling 3 subunits selected from a set of minimally cross-hybridizing4-mers that each differ from one another by three nucleotides. Such anembodiment gives a maximally sized set of 9³, or 729, 12-mers.

Comma-Less Hybridization Tags

In one aspect of the invention, oligonucleotide tags are hybridized totheir complementary sequences, or “anti-tags,” which are attached to asolid phase support, such as a microarray. In such circumstances, it isdesirable to employ oligonucleotide tags that are highly specific foranti-tags that form perfectly matched duplexes between each and everyword of the tag, and that form, at best, only weakly stable duplexeswith anti-tags in which words are not perfectly aligned. That is, inorder to avoid spurious signals, it is desirable select sets of words(and tags constructed from them) that do not form stable duplexes whenhybridized in an imperfectly aligned configuration, e.g. shifted 1 to 2,or more, bases out of perfect alignment. Sets of words with suchproperties may be constructed in several ways, including by inserting“commas” between words or by using words that inherently possess theabove properties, i.e. which result in so-called “comma-less” tags, asdiscussed below. Tags of word having commas are readily constructed fromthe minimally cross-hybridizing sets of words disclosed by Brenner inthe several references cited above. Either comma-containing orcomma-less tags may be used with the invention; however, comma-less tagsare preferred, as they generate the maximum degree of instability in aduplex formed after any small (e.g. 1-3 nucleotide) shift of the tag andanti-tag out of perfect alignment, also sometimes referred to herein asa “change of phase.”

As mentioned above, in tags synthesized combinatorially from shorteroligonucleotide “words,” stable duplexes may form between a tag and itscomplement, even though the “words” are not perfectly aligned. Asillustrated in FIG. 4A, oligonucleotide tag (400) consisting of words(402) through (412) may align perfectly with its complement (414) toform a perfectly matched duplex. However, with some selections of words,there may be other tags in the same repertoire that also form stableduplexes (418), even though the tag (418) is shifted (416), or out ofalignment, by one or more bases with complement (414). The stability ofsuch spurious pairings is very close to that of the perfectly alignedpairings, making it difficult to discriminate between correctlyhybridized tags and incorrectly hybridized tags.

Such spurious hybridizations can be eliminated by designing tags thathave large numbers of mismatches whenever the tag and its complement areshifted one or more bases away from the perfectly aligned configuration.As mentioned above, such designs can be accomplished by eitherintroducing “commas” between words, or by designing words thatinherently have the property that any shift out of perfect alignmentintroduces large numbers of stability-destroying mismatches. In itssimplest form, “commas” may be one or more nucleotides (420) introducedbetween the words (422) of a tag, as illustrated in FIG. 4B. Forexample, the commas (420) of tag (421) may consist of G's, while thewords (422) may consist of only A's, T's, and C's. Thus, for a perfectlymatched duplex to form (i) the commas must be aligned, and (ii) thewords of tag (421) must each be the complement of the words (423) ofcomplement (425). when there is perfect alignment, a perfectly matchduplex (424) is formed. If neither of these conditions is met, then noduplex will form, or if it does form (426), its stability will be vastlylower than that of the perfectly aligned and matched tags (424).

“Commas” may also take the form of words, as illustrated in FIG. 4C.Again, by way of example, the end words (430) of tag (432) may consistof G's, whereas the internal words (434) may consist of A's, C's, andT's. This constrains tag (432) and its complement (436) to be correctlyaligned. As above, absence perfect alignment (438), the stability of anyduplex (440) that may form will be vastly lower than that of a perfectlyaligned tag and its complement.

Finally, repertoires of tags without commas may be constructed fromwords that have the same properties as tags with commas. Such tags withthe “comma-less” property are illustrated in FIG. 4D. That is, in orderto form a perfectly matched duplex between a tag and a complement, thetwo must be perfectly aligned. Words for a repertoire of comma-less tagsmay be constructed in a wide variety of lengths, e.g. such words mayhave lengths in the range of from 4 to 10 nucleotides, and may consistof natural or non-natural nucleotides. In one aspect, words areconstruct from the four natural nucleotides, A, C, G, and T, wheneverthe resulting tags are operated on by enzymes. In another aspect, wordsmay be constructed from nucleotides selected from the group consistingof A, C, G, T, and I, when the resulting tags (or anti-tags) are notprocessed by enzymes. Anti-tags synthesized on a solid phase support maytypically be constructed from a wider variety of nucleotides than tagsthat are processed by enzymes. In one aspect of the invention,comma-less tags may be constructed from the following words.

Consider doublets of the four natural bases. Four sets of such doublets,16 in all, can be defined as follows.

I II III IV GT CT AT AA TG TC TA TT AC AG CG CC CA GA GC GGIn each set, all four differ in both positions from all the othermembers of the set, but when the four different sets are compared witheach other, one base is held in common with one member of the other set.For example, in set I, eight different words can be created by combiningdoublets from set I with doublets from set II in the I-II order and theII-I order. Since each of these sets contain doublets that are thereverse complements of the other, the combinations are made such thatnone of I-II four-base words are the inverse complements of the II-Ifour-base words. Thus, if the I-II words are selected as follows: GTCT,TGTC, ACAG, and CAGA, then the II-I words can be defined only asfollows:

AGCA or AGGT GAAC GATG CTTG CTAC TCGT TCCAan arrangement which conserves the constraint that the members of eachset differs by three bases from any member of the same set. From theabove sets, several sets of words for comma-less tags can beconstructed. Taking the first two sets, an “A” to the end of each wordsof the first set, and a “T” to the end of each word of the second set togive the following:

AGCAT GTCTA GAACT TGTCA CTTGT ACAGA TCGTT CAGAAAlthough the same process does not work with sets III and IV abovebecause in III the doublets are self-complementary, further sets ofwords can be created by switching the I-II into II-I and vice versa, andadding the bases as above, which gives:

CTGTA CAAGT TCTGA ACGAT AGACA TGCTT GACAA GTTCTFor tags not used in enzymatic processing, such as anti-tags synthesizedon a solid phase support, the following sets employing deoxyinosine maybe employed:

AICAT GTCTA GAACT TGTCA CTTGT ACAGA TCITT CAGAA and CTGTA CAAGT TCTGAACIAT AGACA TICTT GACAA GTTCTFurther sets of words for constructing comma-less tags are listed inFIG. 4E.

Oligonucleotide Tags with No Repeat Words

As mentioned above, in some embodiments, it is desirable to decodeoligonucleotide tags sequentially. This requires that theoligonucleotide tags be constructed without repeat words. Sucholigonucleotide tags can be constructed as follows. Let set I ofmutually discriminable di-words consist of GT, TG, CA, and AC, and setII of mutually discriminable di-words consist of GA, AG, CT, and TC.These are combined in two different ways to give two different groups(referred to herein as “languages”) of four dilects, each containingeight words. Language A comprises words of the form: S_(I)-T-S_(II) andS_(II)-A-S_(I) and language B comprises words of the form: S_(I)-A-S_(I)and S_(II)-T-S_(II), where S_(I) is a di-word selected from set I andS_(II) is a di-word selected from set II. The A or T inserted betweenthe di-words gives oligonucleotide tags constructed from such words thecomma-less condition. Writing out the combinations, the following eightgroups of eight-word sets are formed:

Language A Dialect 1 Dialect 2 Dialect 3 Dialect 4 GTTGA GTTAG GTTCTGTTTC TGTAG TGTCT TGTTC TGTGA CATCT CATTC CATGA CATAG ACTTC ACTGA ACTAGACTCT GAATG GAACA GAAAC GAAGT AGACA AGAAC AGAGT AGATG CTAAC CTAGT CTATGCTACA TCAGT TCATG TCACA TCAAC

Language B Dialect 1 Dialect 2 Dialect 3 Dialect 4 GTAGT GTATG GTACAGTAAC TGATG TGACA TGAAC TGAGT CAACA CAAAC CAAGT CAATG ACAAC ACAGT ACATGACACA CTTTC CTTGA CTTAG CTTCT TCTGA TCTAG TCTCT TCTTC GATAG GATCT GATTCGATGA AGTGT AGTTC AGTGA GATAGWithin each dialect, each word differs from the other seven words in 4out of 5 bases. Within each language set A or B, words in one dialectdiffer from those in other dialects by at least two bases out of the 5,some differ by three and some by 4. Between languages A and B, thedialects differ by at least 1 of 5 bases, which is 20% discriminationand some differ by 2, 3, 4, and 5 bases. Thus, oligonucleotide tags canbe constructed from them, either as a set of 4 from each of language Aor language B, or as a full set of 8 from both. 4096 (=8⁴) 4-wordoligonucleotide tags can be constructed from language A (e.g. asA1-A2-A3-A4, where A1 is a word selected from dialect 1 of language A,A2 is a word selected from dialect 2 of language A, and so on). By usingboth language A and B, 16 million (=8⁸) oligonucleotide tags can begenerated (e.g. A1-A2-A3-A4-B1-B2-B3-B4, where A1-A4 are defined asabove, and B1-B4 are defined equivalently). Note that in both cases,only one member is used from each dialect. There are no repeated wordsin the oligonucleotide tags thus constructed.

Tag Complements, Hybridization, and Readout

Preferably, tag complements are synthesized on the surface of a solidphase support, such as a microscopic bead or a specific location on anarray of synthesis locations on a single support, e.g. a microarray,such that populations of identical, or substantially identical,sequences are produced in specific regions. That is, the surface of eachsupport, in the case of a bead, or of each region, in the case of anarray, is derivatized by copies of only one type of tag complementhaving a particular sequence. The population of such beads or regionscontains a repertoire of tag complements each with distinct sequences.As used herein in reference to oligonucleotide tags, includinghybridization tags, tag complements, ligation tags, and the like, theterm “repertoire” means the total number of different tags or tagcomplements in a given set or population.

Solid phase supports containing tag complements may take a variety offorms, e.g. particulate, single-piece and planar, such as a glass slide,and may be composed of a variety of materials, e.g. glass, plastic,silicon, polystyrene, or the like. Particulate solid phase supportsinclude microspheres, such as fluorescently labeled microspheres, e.g.Han et al, Nature Biotechnology, 19: 631-635 (2001); Kettman et al,Cytometry, 33: 234-243 (1998); quantum dots, and the like. In oneaspect, hybridization tags are detected by hybridizing them to theircomplementary sequences on a microarray. Such microarrays may bemanufactured by several alternative techniques, such asphoto-lithographic optical methods, e.g. Pirrung et al, U.S. Pat. No.5,143,854, Fodor et al, U.S. Pat. Nos. 5,800,992; 5,445,934; and5,744,305; fluid channel-delivery methods, e.g. Southern et al, NucleicAcids Research, 20: 1675-1678 and 1679-1684 (1992); Matson et al, U.S.Pat. No. 5,429,807, and Coassin et al, U.S. Pat. Nos. 5,583,211 and5,554,501; spotting methods using functionalized oligonucleotides, e.g.Ghosh et al, U.S. Pat. No. 5,663,242; and Bahl et al, U.S. Pat. No.5,215,882; droplet delivery methods, e.g. Caren et al, U.S. Pat. No.6,323,043; Hughes et al, Nature Biotechnology, 19: 342-347 (2001); andthe like. The above patents disclosing the synthesis of spatiallyaddressable microarrays of oligonucleotides are hereby incorporated byreference. Microarrays used with the invention contain from 50 to500,000 hybridization sites; or from 100 to 250,000 hybridization sites;or from 100 to 40,000 hybridization sites; and preferably, they containfrom 100 to 32,000 hybridization sites; or from 100 to 20,000hybridization sites; or from 100 to 10,000 hybridization sites.

Guidance for selecting conditions and materials for applying labeledoligonucleotide probes to microarrays may be found in the literature,e.g. Wetmur, Crit. Rev. Biochem. Mol. Biol., 26: 227-259 (1991); DeRisiet al, Science, 278: 680-686 (1997); Wang et al, Science, 280: 1077-1082(1998); Duggan et al, Nature Genetics, 21: 10-14 (1999); Schena, Editor,Microarrays: A Practical Approach (IRL Press, Washington, 2000); Hugheset al (cited above); Fan et al, Genomics Research, 10: 853-860 (2000);and like references. These references are hereby incorporated byreference. Typically, application of hybridization tags to a solid phasesupport includes three steps: treatment with a pre-hybridization buffer,treatment with a hybridization buffer that includes the probes, andwashing under stringent conditions. A pre-hybridization step is employedto suppress potential sites for non-specific binding of probe.Preferably, pre-hybridization and hybridization buffers have a saltconcentration of between about 0.8-1.2 M and a pH between about 7.0 and8.3. Preferably, a pre-hybridization buffer comprises one or moreblocking agents such as Denhardt's solution, heparin, fragmenteddenature salmon sperm DNA, bovine serum albumin (BSA), SDS or otherdetergent, and the like. An exemplary pre-hybridization buffer comprises6×SSC (or 6×SSPE), 5×Denhardt's solution, 0.5% SDS, and 100 μg/mldenatured, fragmented salmon sperm DNA, or an equivalentdefined-sequence nucleic acid. Another exemplary pre-hybridizationbuffer comprises 6X-SSPE-T (0.9 M NaCl, 60 mM NaH2PO4, 6 mM EDTA (pH7.4), 0.005% Triton X-100) and 0.5 mg/ml BSA. Pre-hybridization andhybridization buffers may also contain organic solvents, such asformamide to control stringency, tetramethylammonium chloride to negatebase-specific effects, and the like. An exemplary hybridization bufferis SSPE-T. After hybridization, unbound and non-specifically boundoligonucleotide is removed by washing the detection support understringent conditions. Preferably, stringency of the wash solution iscontrolled by temperature, organic solvent concentration, or saltconcentration. More preferably, the stringency of the wash conditionsare determined to be about 2-5° C. below the melting temperature of theisostringency probes at the salt concentration and pH of the washsolution. Preferably, the salt concentration of the wash solution isbetween about 0.01 to 0.1 M.

Exemplary hybridization procedures for applying labeled target sequenceto a GenFlex™ microarray (Affymetrix, Santa Clara, Calif.) is asfollows: denatured labeled target sequence at 95-100° C. for 10 minutesand snap cool on ice for 2-5 minutes. The microarray is pre-hybridizedwith 6×SSPE-T (0.9 M NaCl 60 mM NaH₂,PO₄, 6 mM EDTA (pH 7.4), 0.005%Triton X-100)+0.5 mg/ml of BSA for a few minutes, then hybridized with120 μL hybridization solution (as described below) at 42° C. for 2 hourson a rotisserie, at 40 RPM. Hybridization Solution consists of 3M TMACL(Tetramethylammonium. Chloride), 50 mM MES((2-[N-Morpholino]ethanesulfonic acid) Sodium Salt) (pH 6.7), 0.01% ofTriton X-100, 0.1 mg/ml of Herring Sperm DNA, optionally 50 μM offluorescein-labeled control oligonucleotide, 0.5 mg/ml of BSA (Sigma)and labeled target sequences in a total reaction volume of about 120 Themicroarray is rinsed twice with 1×SSPE-T for about 10 seconds at roomtemperature, then washed with 1×SSPE-T for 15-20 minutes at 40° C. on arotisserie, at 40 RPM. The microarray is then washed 10 times with6×SSPE-T at 22° C. on a fluidic station (e.g. model FS400, Affymetrix,Santa Clara, Calif.). Further processing steps may be required dependingon the nature of the label(s) employed, e.g. direct or indirect.Microarrays containing labeled target sequences may be scanned on aconfocal scanner (such as available commercially from Affymetrix) with aresolution of 60-70 pixels per feature and filters and other settings asappropriate for the labels employed. GeneChip Software (Affymetrix) maybe used to convert the image files into digitized files for further dataanalysis.

Instruments for measuring optical signals, especially fluorescentsignals, from labeled tags hybridized to targets on a microarray aredescribed in the following references which are incorporated byreference: Stem et al, PCT publication WO 95/22058; Resnick et al, U.S.Pat. No. 4,125,828; Karnaukhov et al, U.S. Pat. No. 354,114; Trulson etal, U.S. Pat. No. 5,578,832; Pallas et al, PCT publication WO 98/53300;Brenner et al, Nature Biotechnology, 18: 630-634 (2000); and the like.Methods and apparatus for carrying out repeated and controlledhybridization reactions have been described in U.S. Pat. Nos. 5,871,928,5,874,219, 6,045,996 and 6,386,749, 6,391,623 each of which areincorporated herein by reference.

When tag complements are attached to or synthesized on microbeads, awide variety of solid phase materials may be used with the invention,including microbeads made of controlled pore glass (CPG), highlycross-linked polystyrene, acrylic copolymers, cellulose, nylon, dextran,latex, polyacrolein, and the like, disclosed in the following exemplaryreferences: Meth. Enzymol., Section A, pages 11-147, vol. 44 (AcademicPress, New York, 1976); U.S. Pat. Nos. 4,678,814; 4,413,070; and4,046,720; and Pon, Chapter 19, in Agrawal, editor, Methods in MolecularBiology, Vol. 20, (Humana Press, Totowa, N.J., 1993). Microbead supportsfurther include commercially available nucleoside-derivatized CPG andpolystyrene beads (e.g. available from Applied Biosystems, Foster City,Calif.); derivatized magnetic beads; polystyrene grafted withpolyethylene glycol (e.g., TentaGel™, Rapp Polymere, Tubingen Germany);and the like. Generally, the size and shape of a microbead is notcritical; however, microbeads in the size range of a few, e.g. 1-2, toseveral hundred, e.g. 200-1000 μm diameter are preferable, as theyfacilitate the construction and manipulation of large repertoires ofoligonucleotide tags with minimal reagent and sample usage. Preferably,glycidal methacrylate (GMA) beads available from Bangs Laboratories(Carmel, Ind.) are used as microbeads in the invention. Such microbeadsare useful in a variety of sizes and are available with a variety oflinkage groups for synthesizing tags and/or tag complements.

As mentioned above, in one aspect tag complements comprise PNAs, whichmay be synthesized using methods disclosed in the art, such as Nielsenand Egholm (eds.), Peptide Nucleic Acids: Protocols and Applications(Horizon Scientific Press, Wymondham, UK, 1999); Matysiak et al,Biotechniques, 31: 896-904 (2001); Awasthi et al, Comb. Chem. HighThroughput Screen., 5: 253-259 (2002); Nielsen et al, U.S. Pat. No.5,773,571; Nielsen et al, U.S. Pat. No. 5,766,855; Nielsen et al, U.S.Pat. No. 5,736,336; Nielsen et al, U.S. Pat. No. 5,714,331; Nielsen etal, U.S. Pat. No. 5,539,082; and the like, which references areincorporated herein by reference. Construction and use of microarrayscomprising PNA tag complements are disclosed in Brandt et al, NucleicAcids Research, 31(19), el 19 (2003).

Tagging Polynucleotides

As mentioned above, an important feature of the invention is attachingoligonucleotide tags to polynucleotides, such as fragments from agenome. For simultaneous analysis of fragments from many differentgenomes, fragments from each different genome have the sameoligonucleotide tag attached. In this manner, after a particularanalytical operation has taken place on a mixture, such as extending aprimer, capturing extended primers, or the like, the result on aparticular fragment, or subset of fragments, may be assessed by usingtheir respective oligonucleotide tags, e.g. by labeling, copying, andhybridizing them to a readout platform, such as a microarray. Below, anexample is provided for generating a population of genomic fragmentswherein fragments from each different genome have a differentoligonucleotide tag attached that is comprised of oligonucleotidesubunits, or words.

In one aspect of the invention, all fragments of each genome of apopulation of genomes are labeled with one combination of words selectedfrom a set of eight 5-nucleotide words, or subunits. Thus, whenoligonucleotide tags comprise four such words, a repertoire of 4096oligonucleotide tags is formed; when oligonucleotide tags comprise fivesuch words, a repertoire of 32,768 (=8⁵) oligonucleotide tags is formed;and so on. Once each genome has a unique tag, then common-sequencefragments, e.g. a restriction fragment from a particular locus, can beselected using the method of the invention. The tags may then be used toconvey information about the fragments, e.g. the identity of anucleotide at a particular locus, to a hybridization array for areadout. One of ordinary skill in the art understands that the selectionof 5-word oligonucleotide tags of five nucleotides each and the use ofcommaless tags are design choices that may be varied depending on thegoals and constraints of any particular application. In one embodimentthe following eight-word minimally cross-hydridizing set may be used toconstruct the above repertoire. As described below, preferably, eachword is cloned in a plasmid with additional elements for aiding in theconstruction of oligonucleotide tags.

AGCAT GTCTA GAACT TGACA TCTGT ACGAA CTGTT CATCAUsing these words, 64 di-words are prepared in separate plasmids asdescribed in Brenner and Williams (cited above), which is incorporatedby reference.

A. Single-Word Library and Counting Array Element.

In one embodiment, the single word library contains a ten-base sequence[G/T; G/T; A/T]₃G/T, where “x/T” is an equal mixture of the two bases“x” and “T” at a particular locus. This element encodes a repertoire of1024 (=2¹⁰) different sequences that permits sequences to be counted byhybridization of copies of the sequence to an array of complementarysequences, i.e. a “counting” array. This element is referred to hereinas the “Counting Array” or “CAR” element. In this embodiment, about 30copies of each genome are tagged and each is labeled with one uniquesequence. Thus, if any sorted molecule is found to have a uniquesequence for this array, it is not a genome difference that should havemultiple sequences, and is likely to represent an error in the processwhich has resulted in an altered molecule. Note that however much anyfragment is amplified that it will always possess the original sequencesin the counting array, preserving cardinality as distinct from theconcentration of DNA.

A plasmid having the following characteristics is constructed: (i) noSapI site, and (ii) a sequence of restriction sites:

GGGCCC AGGCCT GGTACC (ApaI) (BspE1) (KpnI)These sites each have “GG” which is absent from tags constructed fromthe words of the above set. Next for each word the strands of followingelement are synthesized (SEQ ID NO: 5):

5′ -pCNNNNNNNNNNGCATCNNNNN [WORD] A 3′ -CCGGGNNNNNNNNNNCGTAGNNNNN [WORD]TCCGGp                   (Sfa N1)where lower case “p” represents a phosphate group. After annealing thestrands, the element is cloned into the above plasmid by cleaving withApaI and Bsp E1. Several plasmids are picked for each word and theclones are sequenced to check the accuracy of the sequence, after whichone is selected for use in tag construction. Elements for the “counting”array are synthesized and also a second primer binding site which willbe required for later amplification. After synthesis, the followingstructure is obtained (SEQ ID NO: 6):

3′-NNNTCCGGA [N₁₅] CCCTG [(G/T; G/T; A/T)₃G/T] GTTGCTTCTCGCCATGGNNNN       BspE1      BsmF1      CAR element           SapI    KpnIUsing the primer “5′-NNNAGGCCT[N₁₅]GGGAC” (SEQ ID NO: 7) the above iscopied, cleaved with KpnI and BspE1, and cloned into each of thesingle-word plasmids. 10⁴ clones of each are isolated to make sure thatall the sequences of the counting array are in the library.

This embodiment is designed to attach tags to fragments generated bycleaving with the “↓GATC” family of restriction endonucleases. Theseenzymes permit the generation of the fragments of several differentlengths:

Average Fragment Enzyme Recognition Site Length Bam HI G↓GATCC   4 KbBam HI + BglII G↓GATCC + G↓GATCT   2 Kb Bst YI R↓GATCY   1 Kb Sau 3a↓GATC 256 bpAll of these leave the same end when cleaved, namely:

5′ -NN     NNCTAGpwhere “p” is a phosphate group. This may be filled in with a single dGTPto give a three-base overhang:

5′ -NNG     NNCTAGpAfter such filling, polynucleotides or cloning vectors cut with SapI(underlined below), which leaves the following ends:

5′- . . . NN GATCGAAGAGC . . .     . . . NNTAGp    GCTTCTCG . . .permits efficient and directional cloning of fragments.

The final construct has the following structure:

. . . [ApaI site]N ₁₀[SfaN1 site]N ₅[word][BspE1 site]N₁₅[BsmF1 site][CAR][SapI site][KpnI site] . . .              Primer X                      Primer Y                      Primer Zwere “N” are arbitrarily selected nucleotides and “CAR” is a countingarray element, as described above.

B. Double-Word Libraries.

Here a library of 64 vectors is disclosed each containing one of the 64possible two-word, or “di-word,” concatenations of words from the 8-wordlibrary flanked by primer binding sites. This double-word library isthen used essentially as described in Brenner and Williams (cited above)to construct oligonucleotide tags. In this embodiment, the firstflanking primer binding site is that shown above as “Primer X,” and theother contains a recognition site for Fold, 5′-GGATG(9/13), whichcontains “GG” and therefore cannot cut any of the words described above.

The following vector elements are synthesized (SEQ ID NO: 8):

5′ -pCN₁₀[SfaN1 site]N₅[word 1] [word 2]N₈CATCC

and (SEQ ID NO: 9):

3′ -CCGGGN₁₀[SfaN1 site]N₅[word1] [word 2]N₉GTAGGCTAGwhere it is understood that the “word 1” and “word 2” refer to both wordsequences and their respective complements. After annealing the abovefragments to form a doublestranded element, it is cloned into a plasmiddigested with ApaI and BamHI. To assure the accuracy of theincorporation, several clones of each “double word” vector are selectedand sequenced. Copies of di-words may be conveniently obtained by PRCusing a biotinylated X primer and another primer.

C. Tagging Genome Fragments.

In this example, a procedure is disclosed for attaching oligonucleotidetags to up to 4096 different genome for simultaneous analysis inaccordance with the invention. The procedure is outlined in FIG. 5.Sixty-four groups of 64 mixtures are formed that each contain fragmentsfrom a single genome, each group of 64 being represented in the figureby arrays (502), (504), and (506) of 64 dots. This is base tier (500) ofsubmixtures where fragments from each genome may be identified by itsposition in such a 64-element array, which may correspond to a well in amulti-well plate, a tube in a rack of tubes, or the like. Intermediatetier of submixtures (510) is formed by attaching a different two-wordtag to each different genome, as described below. The two-word tagidentifies a genome fragment by giving its location within the64-element array of submixtures. To each group of two-word taggedfragments, indicated as g₁AA to g₆₄HH; g₆₅AA to g₁₂₈HH; and so on, adifferent tag A through H is attached and combined (514) to form thefirst mixture (520) in intermediate tier of mixtures (530). The rest ofthe groups of 64 genomes are treated the same to produce additionmixtures of intermediate tier (530), e.g. mixtures containing g₅₁₃AA tog₅₇₆HH; g₅₇₇AA to g₆₄₀HH; and so on, have words added and are combined(516) to form submixture (522); and so on. Tagged fragments insubmixtures (520) to (524) each have a different word attached and arethen combined (532) to form mixture (550) of tagged genomes. Morespecifically, the procedure may be carried out with the following steps.

About 1 ng of human DNA (about 30 copies of the haploid genome) isdigested with Bst Y1 to give fragments of an average size of 1 Kb, afterwhich ends are filled in with dGTP to give 3-base ends as describedabove.

The eight single word libraries, labeled A-H, are amplified and cut withSapI to generate the following single-word fragment:

[ApaI site]N ₁₀[SfaN1 site]N ₅[word][BspE1 site]N ₁₅[BsmF1 site][CAR][ApaI site]N ₁₀[SfaN1 site]N ₅[word][BspE1 site]N₁₅[BsmF1 site][CAR]CTCAp   Primer X                        Primer Y64 genomes are tagged in one batch as follows. 64 reaction vessels arearranged in an 8×8 array wherein each row, 1-8, contains 8 vesselslabeled A-H. To each vessel a different Bst YI-digested genome is added,after which a different single-word fragment, A-H, is added to vessels1-8, in each row to give the following array of reaction vessels withthe following single-word fragments:

Row 1-tube/cell of table (8 tubes/row or 64 tubes in total) 1 g₁A g₂Bg₃C g₄D g₅E g₆F g₇G g₈H 2 g₉A g₁₀B g₁₁C g₁₂D g₁₃E g₁₄F g₁₅G g₁₆H 3 g₁₇Ag₁₈B g₁₉C g₂₀D g₂₁E g₂₂F g₂₃G g₂₄H 4 g₂₅A g₂₆B g₂₇C g₂₈D g₂₉E g₃₀F g₃₁Gg₃₂H 5 g₃₃A g₃₄B g₃₅C g₃₆D g₃₇E g₃₈F g₃₉G g₄₀H 6 g₄₁A g₄₂B g₄₃C g₄₄Dg₄₅E g₄₆F g₄₇G g₄₈H 7 g₄₉A g₅₀B g₅₁C g₅₂D g₅₃E g₅₄F g₅₅G g₅₆H 8 g₅₇Ag₅₈B g₅₉C g₆₀D g₆₁E g₆₂F g₆₃G g₆₄Hwhere “g_(k)” is a fragment from genome K

The single-word fragments are ligated to the genome fragments to givegenome fragments having single-word fragments on both ends. Thesefragments are processed as follows so that a single word is on only oneend. First, the reaction constituents from every vessel in each row arepooled so that eight mixed samples are obtained.

Row (Tube) Resulting Mixtures (1-tube/row) 1 g₁A g₂B g₃C g₄D g₅E g₆F g₇Gg₈H 2 g₉A g₁₀B g₁₁C g₁₂D g₁₃E g₁₄F g₁₅G g₁₆H 3 g₁₇A g₁₈B g₁₉C g₂₀D g₂₁Eg₂₂F g₂₃G g₂₄H 4 g₂₅A g₂₆B g₂₇C g₂₈D g₂₉E g₃₀F g₃₁G g₃₂H 5 g₃₃A g₃₄Bg₃₅C g₃₆D g₃₇E g₃₈F g₃₉G g₄₀H 6 g₄₁A g₄₂B g₄₃C g₄₄D g₄₅E g₄₆F g₄₇G g₄₈H7 g₄₉A g₅₀B g₅₁C g₅₂D g₅₃E g₅₄F g₅₅G g₅₆H 8 g₅₇A g₅₈B g₅₉C g₆₀D g₆₁Eg₆₂F g₆₃G g₆₄HThe DNA of each of the eight vessels is denatured and Primer Y(pAGGCCTN₁₅GGGAC) (SEQ ID NO: 10) is added to prime the 3′ tag sequenceof each of the single strands as follows (SEQ ID NO: 11 AND SEQ ID NO:12):

AGGCCTN₁₅GGGAC TCCGGAN₁₅CCCTG[CAR]CTAG[fragment]CTAG [CAR]GTCCC . . .The primer is extended using 5-Me-dCTP to give the following (SEQ ID NO:13 AND SEQ ID NO: 14):

AGGCCTN₁₅GGGAC[CAR]GATC(Me)[fragment]GATC(Me)[CAR]GTC(Me)C(Me)C(Me) . . .TCCGGAN₁₅CCCTG[CAR]CTAG    [fragment]CTAG    [CAR]CAG    G    G . . .All of the BsmF1 sites of the fragments are protected by halfmethylation, except for the site to the left of the tag. When thefragments are cleaved with BsmF1, the left tag is removed up to the“GATC” site, leaving the following (SEQ ID NO: 15):

which results in the following:

GATC[fragment]GATC[CAR][BsmF1 site][Primer Y][word]N₅[SfaN1 site][Primer X]    [fragment]CTAG[CAR][BsmF1 site][Primer Y][word]N₅[SfaN1 site][Primer X]The “GATC” overhang is filled in with dGTP and ligated to the followingadaptor containing a primer binding site for sequencing (SEQ ID NO: 16):

N₂₀GC^(Me) ATCAG N₂₀CG TAGTCTAGpThe methylated C in the upper strand protects the lefthand site whilethe right hand portion of the fragments are manipulated. Words are addedas follows. First, the C's of the bottom strand are replaced with5-methyl-C's. This is accomplished by denaturing the above fragments,priming with a biotinylated Primer X (5′-biotin-GGGCCCN₁₀[Sfa N1site]N₅), copying with 5-Me-CTP, and removing the strands withavidinated support. The fragments are released by cleaving with Sfa N1to give in each of the eight vessels the sequences:

[fragment]GATC[CAR][Primer Y]W [fragment]CTAG[CAR][Primer Y]WWWWWpwhere all eight words are represented in the overhang and “W” representsa nucleotide of a word or its complement. Next the di-word libraries arepooled, cleaved with FokI, then ligated to the above fragment to add thenext word. The process is continued as outlined below until the desirednumber of words is added to the genomic fragments to complete the tags.Thus, by this method, 64 genomes at a time may be tagged.

Returning to the table immediately above, in each of the sixty-four64-genome collections, a different word is added to each different row,e.g. A→Row 1, B→Row 2, etc., to produce the following mixtures:

Row (Tube) Resulting Mixtures 1 g₁AA g₂BA g₃CA g₄DA g₅EA g₆FA g₇GA g₈HA2 g₉AB g₁₀BB g₁₁CB g₁₂DB g₁₃EB g₁₄FB g₁₅GB g₁₆HB 3 g₁₇AC g₁₈BC g₁₉CCg₂₀DC g₂₁EC g₂₂FC g₂₃GC g₂₄HC 4 g₂₅AD g₂₆BD g₂₇CD g₂₈DD g₂₉ED g₃₀FDg₃₁GD g₃₂HD 5 g₃₃AE g₃₄BE g₃₅CE g₃₆DE g₃₇EE g₃₈FE g₃₉GE g₄₀HE 6 g₄₁AFg₄₂BF g₄₃CF g₄₄DF g₄₅EF g₄₆FF g₄₇GF g₄₈HF 7 g₄₉AG g₅₀BG g₅₁CG g₅₂DGg₅₃EG g₅₄FG g₅₅GG g₅₆HG 8 g₅₇AH g₅₈BH g₅₉CH g₆₀DH g₆₁EH g₆₂FH g₆₃GHg₆₄HH

These are combined to form a mixture designated as g₁₋₆₄(AA-HH), where“AA-HH” means all 64 di-words from AA to HH. The same operation isseparately carried out for every one of the sixty-four batches of 64genomes each, i.e. genomes 65-128, 129-192, . . . and 448-512 to givethe following 8 mixtures:

-   -   g₉₁-g₆₄ (AA-HH)    -   g₆₅-g₁₂₈ (AA-HH)    -   g₁₂₉-g₁₉₂ (AA-HH)    -   g₁₉₃-g₂₅₆ (AA-HH)    -   g₂₅₇-g₃₂₀ (AA-HH)    -   g₃₂₁-g₃₈₄ (AA-HH)    -   g₃₈₅-g₄₄₈ (AA-HH)    -   g₄₄₉-g₅₁₂ (AA-HH)        As above, a different word is attached to each fragment in each        of the different mixtures to give the following:

Row (Tube) Operation Resulting Mixtures 1 A→ g₁₋₆₄(AA-HH) g₁₋₆₄(AAA-HHA)2 B→ g₆₅₋₁₂₈(AA-HH) g₆₅₋₁₂₈(AAB-HHB) 3 C→ g₁₂₉₋₁₉₂(AA-HH)g₁₂₉₋₁₉₂(AAC-HHC) 4 D→ g₁₉₃₋₂₅₆(AA-HH) g₁₉₃₋₂₅₆(AAD-HHD) 5 E→g₂₅₇₋₃₂₀(AA-HH) g₂₅₇₋₃₂₀(AAE-HHE) 6 F→ g₃₂₁₋₃₈₄(AA-HH) g₃₂₁₋₃₈₄(AAF-HHF)7 G→ g₃₈₅₋₄₄₈(AA-HH) g₃₈₅₋₄₄₈(AAG-HHG) 8 H→ g₄₄₉₋₅₁₂(AA-HH)g₄₄₉₋₅₁₂(AAH-HHH)where “AAA-HHH” means all 8³ (=512) tri-words from AAA to HHH. Again, adifferent word is attached to each fragment in each of the differentthree-word tagged fragment mixtures, which are then combined to form thefinal mixture (550), as shown in FIG. 5.

1-21. (canceled)
 22. A composition of nucleic acid molecules made by thefollowing method: ligating a discriminatory oligonucleotide tag tofragmented genomic DNA so that substantially every target polynucleotidein said fragmented genomic DNA receives a tag that comprises a uniquenucleotide sequence, to produce a tagged sample; and amplifying thetarget polynucleotides in said tagged sample by polymerase chainreaction to produce a plurality of amplicons that each comprise a uniquetag.
 23. The method of claim 22, wherein said fragmented genomic DNA isfragmented by digestion with a restriction enzyme.
 24. The method ofclaim 22, wherein said fragmented genomic DNA is fragmented mammaliangenomic DNA.